title: LDG_06_PPAR_CD10_neg [RNA-seq]

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description:
R51
Exp ID: 180611_0143_s18
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx

data_processing:
Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.

source_name: Human whole blood

extract_protocol:
Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.

tag: diagnosis

value: Lupus

tag: cell type

value: LDG


title: Sample75_590289: D00000000205673_DAY 1_Etanercept

status: Public on Nov 22 2019

type: protein

city: New York

first: Lewis

middle: Elwood

last: Tomalin

state: New York

address: 303 East 71st Street, Apt1B

department: Population Health Science & Policy

country: USA

institute: Icahn School of Medicine at Mount Sinai

scan_protocol: Detection and quantification of the resulting DNA sequences was performed using microfluidic real-time quantitative PCR chip (96.96, Dynamic Array IFC, Fluidigm Biomark, South San Francisco, CA).

label: oligonucleotide-labeled antibody

molecule: protein

organism: Homo sapiens

source_name: Blood_DAY 1_Etanercept

treatment_protocol: Patients were treated with either tofacitinib 10mg QD or etanercept 50mg BIW as described in ClinicalTrials.gov: NCT01241591 and Bachelez et al., 2015

tag: visit

value: DAY 1

tag: treatment

value: Etanercept 50 mg BIW

tag: treatmentshort

value: Etanercept

tag: pasi

tag: tag

value: R

tag: age

tag: gender

value: F

tag: platesimple

tag: plate


title: Sample74_601368: D00000000205663_DAY 1_Etanercept

data_processing: Detection and quantification of the resulting DNA sequences was performed using microfluidic real-time quantitative PCR chip (96.96, Dynamic Array IFC, Fluidigm Biomark, South San Francisco, CA).

value: M


title: Sample86_603656: D00000000205719_WEEK 4_Tofacitinib

source_name: Blood_WEEK 4_Tofacitinib

value: WEEK 4

value: Tofacitinib


title: LDG_04_PPAR_CD10_neg [RNA-seq]

type: SRA

description:
R49
Exp ID: 180611_0143_s15
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx

library_source: transcriptomic

molecule: total RNA


title: LDG_05_PPAR_CD10_neg [RNA-seq]

description:
R50
Exp ID: 180611_0143_s17
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: LDG_03_LE_CD10_neg [RNA-seq]

description:
R48
Exp ID: 180611_0143_s16
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: Sample85_601376: D00000000205715_WEEK 4_Tofacitinib


title: Sample73_595682: D00000000205786_DAY 1_Tofacitinib

source_name: Blood_DAY 1_Tofacitinib


title: Sample72_598436: D00000000205708_DAY 1_Etanercept


title: LDG_02_LE_CD10_neg [RNA-seq]

description:
R47
Exp ID: 180611_0143_s14
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: Sample71_598916: D00000000205775_WEEK 4_Tofacitinib


title: Sample83_601296: D00000000205763_WEEK 4_Tofacitinib


title: Sample69_597806: D00000000205771_WEEK 4_Tofacitinib


title: Sample76_609666: D00000000205615_DAY 1_Tofacitinib

value: NR


title: LDG_01_LE_CD10_neg [RNA-seq]

description:
R46
Exp ID: 180611_0143_s13
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: Sample81_599258: D00000000205726_WEEK 4_Etanercept

source_name: Blood_WEEK 4_Etanercept


title: wt_heart_1

city: Cambridge

first: Abbie

last: Groff

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

description: All mice used for the study are Tug1_tm1.1Vlcg mice (wild types contain 2 normal Tug1 alleles (no LacZ) and homozygous knockout have a lacZ reporter in place of Tug1 on both alleles.)

data_processing:
Casava 1.8.2 was used to call bases
Reads were aligned to mm10 using tophat2 (--no-coverage-search --max-multihits 10 -p 8)
Bams were quantified using cuffquant and a modified verson of the GENCODE M2 transcriptome (--no-update-check -p 8)
Differential analysis was performed using cuffdiff2 (-p 8)
Genome_build: mm10
Supplementary_files_format_and_content: text file with cuffdiff output

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Tissues were harvested immediately after euthanasia, snap frozen in liquid nitrogen and stored at -80˚C. Tissues were subsequently pulverized in liquid nitrogen and homogenized in TRIzol. Embryonic Mouse Fibroblasts (MEF, passage 2) were cultured in 10cm dishes in normal conditions (37˚C, 5% CO2) and homogenized directly in Trizol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)

tag: tissue

value: heart

tag: lncrna previous name

tag: background

value: C57BL/6J (N3-C57BL/6J, no Neo)

tag: official strain name

tag: genotype

value: wt

tag: Sex


title: ko_heart_0

value: ko


title: Sample82_598868: D00000000205801_DAY 1_Tofacitinib


title: Sample68_606874: D00000000205617_DAY 1_Etanercept


title: treated IL-6 RSkMC -rep 2

type: RNA

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

hyb_protocol: Each Cyanine-3-labeled RNA samples were hybridized onto microarray for 20h at 55°C in hybridization rotating oven (Agilent Technologies).

scan_protocol: Acquisition and analysis of hybridization intensities were performed using Agilent DNA Microarray Scanner G2505C. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: The scanned images were analyzed with Feature Extraction Software (version 10.10.1.1) using default parameters (protocol miRNA_1010_Sep10 and Grid: 046066_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Rat primary skeletal muscle cells (RSkMC)

label_protocol: One hundred ng of total RNA with miRNA Spike-In (microRNA Spike-In Kit, Agilent Technologies) added were taken for labeling reaction. miRNA was labeled with Cyanine 3-pCp using the Complete Labeling and Hyb Kit (Agilent Technologies) according to the manufacturer’s procedure. The labeled RNA samples were purified on Micro Bio-Spin 6 columns to remove DMSO and unbound Cyanine 3-pCp.

growth_protocol: Cell cultures were maintained free of contamination at the exponential growth phase in 10% FBS/DMEM (Fetal Bovine Serum/Dulbecco’s modified Eagle’s medium, Gibco MA, USA) supplemented with an antibiotic-antimycotic mixture (Life Technologies) in controlled humidified air with 5% CO2, at 37°C. The growth medium was changed every other day. When the cells reached ~80% confluence, myogenic differentiation was induced after switching to a medium containing 2% HS (Horse serum, Gibco MA, USA). Cells were subjected to 11 days of differentiation in the presense of IL-6 (recombinant, expressed in E.coli and suitable for cell culture, final concentration – 1 ng/ml, Sigma-Aldrich, St. Louis, MO, USA) and were used for the study.

extract_protocol: Total RNA, which also included miRNA, was isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s procedure. RNA quality was determined using Agilent 2100 Bioanalyzer (USA) and RNA 6000 Nano Kit (Agilent, Germany). All RNA samples taken for microarray analysis were of high quality (RIN was  between 9.5 and 10.0).

value: RSkMC are isolated from the limbal skeletal muscle of neonates and cryopreserved at second passage were purchased from European Collection of Animal Cell Culture (ECACC).

tag: developmental stage

value: cell cultures on 11th day after induction of differentiation


title: LDG_06_PPAR_CD10_pos [RNA-seq]

description:
R45
Exp ID: 180611_0143_s12
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx

tag: diagnosis

value: Lupus

tag: cell type


title: LDG_05_PPAR_CD10_pos [RNA-seq]

description:
R44
Exp ID: 180611_0143_s11
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx

value: LDG


title: Sample80_599034: D00000000205693_WEEK 4_Etanercept

tag: visit

tag: treatment


title: Sample79_602048: D00000000205645_WEEK 4_Tofacitinib

tag: treatmentshort

tag: pasi


title: treated IL-6 RSkMC -rep 1


title: treated IL-6 RSkMC -rep 3


title: Sample67_603694: D00000000205712_WEEK 4_Tofacitinib

tag: tag

tag: age


title: Sample66_602018: D00000000205673_WEEK 4_Etanercept

tag: gender

tag: platesimple


title: treated IL-6 RSkMC -rep 4


title: LDG_03_LE_CD10_pos [RNA-seq]

description:
R42
Exp ID: 180611_0143_s10
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: Sample65_602594: D00000000205567_DAY 1_Tofacitinib

value: DAY 1

tag: plate


title: Sample77_590289: D00000000205673_DAY 1_Etanercept

value: Etanercept 50 mg BIW


title: LDG_02_LE_CD10_pos [RNA-seq]

description:
R41
Exp ID: 180611_0143_s09
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: Sample78_609666: D00000000205615_DAY 1_Tofacitinib


title: control RSkMC -rep 2


title: Sample64_610432: D00000000205688_DAY 1_Etanercept

value: Etanercept


title: LDG_01_LE_CD10_pos [RNA-seq]

description:
R40
Exp ID: 180611_0143_s08
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: control RSkMC -rep 3


title: NDN_06_PPAR [RNA-seq]

description:
R39
Exp ID: 180611_0143_s05
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx

value: NDN


title: Sample76_601368: D00000000205663_DAY 1_Etanercept

value: R


title: Sample63_600468: D00000000205641_DAY 1_Etanercept

value: M


title: Sample75_595682: D00000000205786_DAY 1_Tofacitinib


title: Sample62_603182: D00000000205603_WEEK 4_Etanercept

value: WEEK 4


title: Sample74_598436: D00000000205708_DAY 1_Etanercept

value: F


title: LDG_04_PPAR_CD10_pos [RNA-seq]

description:
R43
Exp ID: 180611_0143_s07
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: NDN_04_PPAR [RNA-seq]

description:
R37
Exp ID: 180611_0143_s03
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: NDN_05_PPAR [RNA-seq]

description:
R38
Exp ID: 180611_0143_s04
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: Sample73_598916: D00000000205775_WEEK 4_Tofacitinib

value: Tofacitinib


title: Sample71_597806: D00000000205771_WEEK 4_Tofacitinib


title: Sample59_602364: D00000000205758_DAY 1_Etanercept

value: NR


title: Sample60_609710: D00000000205749_WEEK 4_Tofacitinib


title: ZsGreenPositive_replicate2 [ZsG_rep2]

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

data_processing:
The Kallisto pseudoaligner, version 0.46, (Bray et al., 2016) was used to map raw reads to the reference transcriptomes from mouse (Ensembl GRCm38, release 79).
Kallisto quantification results were inported into the R programming environment using the TxImport package (Soneson et al., 2015), and analysis was performed using the  Bioconductor suite of packages (Huber et al., 2015).
The EdgeR package (Robinson et al., 2010) and the Trimmed Mean of M-values (TMM) method (Robinson and Oshlack, 2010) were used for normalization
The Limma package (Ritchie et al., 2015) was used for differential gene testing with mean-variance modeling carried out using VOOM (Law et al., 2014).
Genome_build: Release 46 of Toxoplasma gondii ME49 strain reference transcriptome (annotated transcripts)
Supplementary_files_format_and_content: tab-delimited text files of log2 counts per million (CPM) for each gene in each sample

source_name: ZsGreenPositive

growth_protocol: Bystander, infected, and injected large peritoneal macrophages were sort purified from peritoneal exudate cells (PECs) using a FACSAria III (BD Biosciences; device: 5 mL tubes; precision: single-cell; nozzle: 100 μm). Forward-scatter area (FCS-A) versus side-scatter area (SSC-A) was used to exclude damaged cells, dead cells were stained with LIVE/DEAD™ Fixable Aqua. 50,000 cells were sorted into different 5 mL tubes filled with 700 uL Cell lysis buffer TLR (Qiagen) for RNA extraction and stored at −80 °C.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded mRNA  Kit, according to the manufacturer’s instructions.

treatment_protocol: Mice were infected with 10^6 T. gondii and large peritoneal macrophages were sorted 24 hours after infection.

tag: strain background

tag: genotype/variation

value: Large peritoneal macrophages

tag: sorted fraction

value: injected


title: ZsGreenPositive_replicate4 [ZsG_rep4]


title: ZsGreenPositive_replicate3 [ZsG_rep3]


title: Sample70_606874: D00000000205617_DAY 1_Etanercept


title: NDN_03_LE [RNA-seq]

description:
R36
Exp ID: 180611_0143_s06
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: NDN_02_LE [RNA-seq]

description:
R35
Exp ID: 180611_0143_s02
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: ZsGreenPositive_replicate1 [ZsG_rep1]


title: Sample69_603694: D00000000205712_WEEK 4_Tofacitinib


title: NDN_01_LE [RNA-seq]

description:
R34
Exp ID: 180611_0143_s01
mRNA
processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx


title: control RSkMC -rep 1


title: DoublePositive_replicate4 [DP_rep4]

source_name: DoublePositive

value: infected


title: Sample61_600668: D00000000205708_WEEK 4_Etanercept


title: Sample56_606854: D00000000205607_DAY 1_Tofacitinib


title: DoublePositive_replicate3 [DP_rep3]


title: Sample55_603678: D00000000205690_WEEK 4_Etanercept


title: Sample67_602594: D00000000205567_DAY 1_Tofacitinib


title: LDG_SLE_10_mat [RNA-seq]

description:
R32
Exp ID: 161229_0016_s25
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample54_603068: D00000000205603_DAY 1_Etanercept


title: LDG_SLE_11_mat [RNA-seq]

description:
R33
Exp ID: 161229_0016_s27
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample65_600468: D00000000205641_DAY 1_Etanercept


title: DoublePositive_replicate2 [DP_rep2]


title: LDG_SLE_09_mat [RNA-seq]

description:
R31
Exp ID: 161229_0016_s24
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: DoublePositive_replicate1 [DP_rep1]


title: Sample53_595636: D00000000205654_WEEK 4_Tofacitinib


title: LDG_SLE_08_mat [RNA-seq]

description:
R30
Exp ID: 161229_0016_s19
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample57_585328: D00000000205763_DAY 1_Tofacitinib


title: DoubleNegative_replicate4 [DN_rep4]

source_name: DoubleNegative

value: bystander


title: Sample63_600668: D00000000205708_WEEK 4_Etanercept


title: Sample62_609710: D00000000205749_WEEK 4_Tofacitinib


title: DoubleNegative_replicate3 [DN_rep3]


title: Sample52_601460: D00000000205567_WEEK 4_Tofacitinib


title: Sample68_602018: D00000000205673_WEEK 4_Etanercept


title: LDG_SLE_06_imm [RNA-seq]

description:
R28
Exp ID: 161229_0016_s14
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample51_609696: D00000000205688_WEEK 4_Etanercept


title: DoubleNegative_replicate2 [DN_rep2]


title: Sample50_590200: D00000000205645_DAY 1_Tofacitinib


title: LDG_SLE_07_imm [RNA-seq]

description:
R29
Exp ID: 161229_0016_s18
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: DoubleNegative_replicate1 [DN_rep1]


title: IL4_IFNG_treated_replicate2

description:
IL4_IFNG_rep2
IFNG-IL4-2_S12_mergedLanes

data_processing:
The Kallisto pseudoaligner, version 0.46, (Bray et al., 2016) was used to map raw reads to the reference transcriptomes from mouse (Ensembl GRCm38, release 98)
Kallisto quantification results were inported into the R programming environment using the TxImport package (Soneson et al., 2015), and analysis was performed using the  Bioconductor suite of packages (Huber et al., 2015).
The EdgeR package (Robinson et al., 2010) and the Trimmed Mean of M-values (TMM) method (Robinson and Oshlack, 2010) were used for normalization
The Limma package (Ritchie et al., 2015) was used for differential gene testing with mean-variance modeling carried out using VOOM (Law et al., 2014).
Genome_build: Release 98 of mouse reference transcriptome GRCm38
Supplementary_files_format_and_content: tab-delimited text files of log2 counts per million (CPM) for each gene in each sample

growth_protocol: WT mice were used to generate bone marrow derived macrophages (BMMøs). Red blood cells (RBCs) were lysed with 0.86% ammonium chloride. Bone marrow cells were then plated at a concentration of 2 × 106 cells per 10 mL of media in 100 mm plates. For BMMøs, macrophage medium was composed of DMEM supplemented with 10% serum, 25 mM HEPES, 1% penicillin-streptomycin, 1 mM sodium pyruvate [Gibco], 0.1% β-mercaptoethanol, and 30% L929 supernatant. Media was replenished on days 3 and 6. Between days 7 and 9, cells were harvested using ice-cold PBS with 5 μM EDTA.

treatment_protocol: To induce M1, M2a and M2c macrophage subtypes, BMMø were stimulated for 24 hours with IFN-γ (10 ng/mL), IL-4 (10 ng/mL) or IL-10 (10 ng/mL) respectively.

value: wild-type

value: bone marrow-derived macrophages (BMDM)

value: stimulated


title: Sample48_600430: D00000000205796_WEEK 4_Etanercept


title: Sample59_585328: D00000000205763_DAY 1_Tofacitinib

value: DAY 1


title: Sample61_602364: D00000000205758_DAY 1_Etanercept

value: Etanercept 50 mg BIW


title: LDG_SLE_04_mat [RNA-seq]

description:
R26
Exp ID: 161229_0016_s06
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx

value: Lupus

value: LDG


title: Sample64_603182: D00000000205603_WEEK 4_Etanercept

value: Etanercept

value: R


title: Sample7_598998: D00000000205963_WEEK 4_Tofacitinib

value: WEEK 4

value: M


title: Sample47_601670: D00000000205768_WEEK 4_Etanercept


title: LDG_SLE_03_mat [RNA-seq]

description:
R25
Exp ID: 170208_0025_s05
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample57_603678: D00000000205690_WEEK 4_Etanercept


title: Sample58_606854: D00000000205607_DAY 1_Tofacitinib

value: Tofacitinib


title: IL4_IFNG_treated_replicate1

description:
IL4_IFNG_rep1
IFNG-IL4-1_S6_mergedLanes


title: IFNG_treated_replicate2

description:
IFNG_rep2
IFNG-2_S11_mergedLanes


title: Sample45_589342: D00000000205750_DAY 1_Tofacitinib

value: NR

value: F


title: Sample56_603068: D00000000205603_DAY 1_Etanercept


title: LDG_SLE_01_mat [RNA-seq]

description:
R23
Exp ID: 161229_0016_s03
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample44_603040: D00000000205594_WEEK 4_Tofacitinib


title: IL4-IL10_treated_replicate2

description:
IL4_IL10_rep2
IL4-IL10-2_S10_mergedLanes


title: NDN_SLE_11 [RNA-seq]

description:
R22
Exp ID: 161229_0016_s26
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx

value: NDN


title: Sample55_595636: D00000000205654_WEEK 4_Tofacitinib


title: Sample49_607174: D00000000205813_DAY 1_Etanercept


title: Sample54_601460: D00000000205567_WEEK 4_Tofacitinib


title: Sample42_607622: D00000000205679_DAY 1_Tofacitinib


title: LDG_SLE_05_mat [RNA-seq]

description:
R27
Exp ID: 161229_0016_s11
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample53_609696: D00000000205688_WEEK 4_Etanercept


title: Sample43_602804: D00000000205699_WEEK 4_Tofacitinib


title: IL10_treated_replicate2

description:
IL10_rep2
IL10-2_S9_mergedLanes


title: NDN_SLE_09 [RNA-seq]

description:
R20
Exp ID: 161229_0016_s22
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: NDN_SLE_08 [RNA-seq]

description:
R19
Exp ID: 161229_0016_s17
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample41_601762: D00000000205663_WEEK 4_Etanercept


title: IL10_treated_replicate1

description:
IL10_rep1
IL10-1_S3_mergedLanes


title: Sample52_590200: D00000000205645_DAY 1_Tofacitinib


title: Sample51_607174: D00000000205813_DAY 1_Etanercept


title: LDG_SLE_02_imm [RNA-seq]

description:
R24
Exp ID: 161229_0016_s05
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: IL4_treated_replicate2

description:
IL4_rep2
IL4-2_S8_mergedLanes


title: IFNG_treated_replicate1

description:
IFNG_rep1
IFNG-1_S5_mergedLanes


title: Sample50_600430: D00000000205796_WEEK 4_Etanercept


title: Sample39_599152: D00000000205621_WEEK 4_Etanercept


title: NDN_SLE_06 [RNA-seq]

description:
R17
Exp ID: 161229_0016_s10
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample40_590136: D00000000205690_DAY 1_Etanercept


title: IL4_treated_replicate1

description:
IL4_rep1
IL4-1_S2_mergedLanes


title: Sample49_601670: D00000000205768_WEEK 4_Etanercept


title: Sample38_600426: D00000000205758_WEEK 4_Etanercept


title: NDN_SLE_05 [RNA-seq]

description:
R16
Exp ID: 161229_0016_s09
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: NDN_SLE_10 [RNA-seq]

description:
R21
Exp ID: 161229_0016_s23
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample37_601140: D00000000205768_DAY 1_Etanercept


title: NDN_SLE_04 [RNA-seq]

description:
R15
Exp ID: 170208_0025_s07
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: NDN_SLE_07 [RNA-seq]

description:
R18
Exp ID: 161229_0016_s13
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: IL4-IL10_treated_replicate1

description:
IL4_IL10_rep1
IL4-IL10-1_S4_mergedLanes


title: Sample36_595720: D00000000205741_WEEK 4_Etanercept


title: Sample47_589342: D00000000205750_DAY 1_Tofacitinib


title: WT3

city: Prague 4

first: Josef

last: Pasulka

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

description: Pair-end, non-stranded

data_processing:
All RNA-seq datasets were mapped using STAR 2.5.3a
Mapped reads were counted using program featureCounts
The GENCODE gene set (GENCODE M15) was used for the annotation
See the methods for more details
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing gene counts generated by “featureCounts” program

source_name: GV oocyte

extract_protocol:
NGS libraries were generated using V2 version of Ovation RNA-seq kit from Nugen. Libraries were prepared according to manufacturer’s protocol. cDNA fragmentation was performed on Bioruptor sonication device (Diagenode) as follows: 45 s ON, 30 s OFF for 21 cycles on low intensity, 100 ng fragmented cDNA was used for further library preparation. Libraries were amplified by 9 cycles of PCR. Libraries were quantified by Qubit HS DNA kit, quality was assessed on 2100 Bioanalyzer HS DNA chip.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: Mili-DAH/WT, Dicer-SOM/WT

tag: tissue

value: GV oocyte

tag: age (weeks)


title: Sample35_601386: D00000000205759_DAY 1_Tofacitinib


title: Sample46_603040: D00000000205594_WEEK 4_Tofacitinib


title: unstimulated_control_replicate1

description:
unstim_rep1
Unstimulated-1_S1_mergedLanes

value: wild-type

tag: cell type

value: untreated


title: NDN_SLE_03 [RNA-seq]

description:
R14
Exp ID: 161229_0016_s04
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx

tag: diagnosis


title: Sample33_606964: D00000000205813_WEEK 4_Etanercept

tag: visit

tag: treatment


title: NDN_SLE_02 [RNA-seq]

description:
R13
Exp ID: 170208_0025_s03
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample43_601762: D00000000205663_WEEK 4_Etanercept

tag: treatmentshort

tag: pasi


title: Sample32_602812: D00000000205575_WEEK 4_Etanercept

tag: tag

tag: age


title: Sample45_602804: D00000000205699_WEEK 4_Tofacitinib

tag: gender

tag: platesimple


title: NDN_SLE_01 [RNA-seq]

description:
R12
Exp ID: 161229_0016_s01
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: WT2o

description: Pair-end, non-stranded


title: Sample42_590136: D00000000205690_DAY 1_Etanercept

tag: plate


title: WT2

description: Pair-end, non-stranded


title: WT1o

description: Pair-end, non-stranded


title: Sample31_602752: D00000000205715_DAY 1_Tofacitinib


title: NDN_ctrl_10 [RNA-seq]

description:
R10
Exp ID: 161229_0016_s20
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx

value: Healthy (control)


title: Sample41_599152: D00000000205621_WEEK 4_Etanercept


title: unstimulated_control_replicate2

description:
unstim_rep2
Unstimulated-2_S7_mergedLanes

tag: strain background

tag: genotype/variation

value: bone marrow-derived macrophages (BMDM)


title: NDN_ctrl_09 [RNA-seq]

description:
R09
Exp ID: 161229_0016_s16
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: SOM1_new

description: Pair-end, non-stranded

tag: strain

value: Mili-DAH/WT, Dicer-SOM/SOM


title: Sample28_599106: D00000000205582_WEEK 4_Tofacitinib


title: Sample40_600426: D00000000205758_WEEK 4_Etanercept

value: Etanercept 50 mg BIW


title: SOM2_new

description: Pair-end, non-stranded

tag: genotype


title: NDN_ctrl_08 [RNA-seq]

description:
R08
Exp ID: 161229_0016_s15
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample38_595720: D00000000205741_WEEK 4_Etanercept


title: NDN_ctrl_07 [RNA-seq]

description:
R07
Exp ID: 161229_0016_s12
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample37_601386: D00000000205759_DAY 1_Tofacitinib

value: DAY 1


title: Sample26_600672: D00000000205701_WEEK 4_Tofacitinib


title: NDN_ctrl_06 [RNA-seq]

description:
R06
Exp ID: 170208_0025_s11
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: MILI2

description: Pair-end, non-stranded

value: Mili-DAH/DAH, Dicer-SOM/WT

tag: tissue


title: DBL1

description: Pair-end, non-stranded

value: Mili-DAH/DAH, Dicer-SOM/SOM

tag: age (weeks)


title: NDN_ctrl_11 [RNA-seq]

description:
R11
Exp ID: 161229_0016_s21
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx

tag: cell type


title: Sample27_599194: D00000000205587_WEEK 4_Tofacitinib

value: WEEK 4

value: R


title: NDN_ctrl_05 [RNA-seq]

description:
R05
Exp ID: 170208_0025_s09
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx

tag: diagnosis


title: Sample24_595758: D00000000205775_DAY 1_Tofacitinib

tag: visit

value: Tofacitinib

value: M


title: Sample30_600844: D00000000205596_WEEK 4_Tofacitinib

tag: treatment


title: DBL2o

description: Pair-end, non-stranded


title: Sample25_602100: D00000000205750_WEEK 4_Tofacitinib

tag: treatmentshort

value: NR

value: F


title: DBL1o

description: Pair-end, non-stranded


title: Sample33_602752: D00000000205715_DAY 1_Tofacitinib

tag: pasi


title: Sample23_597338: D00000000205741_DAY 1_Etanercept

value: Etanercept

tag: tag


title: Sample39_601140: D00000000205768_DAY 1_Etanercept

tag: age


title: Sample22_599132: D00000000205801_WEEK 4_Tofacitinib

tag: gender


title: Sample32_600844: D00000000205596_WEEK 4_Tofacitinib

tag: platesimple


title: NDN_ctrl_03 [RNA-seq]

description:
R03
Exp ID: 161229_0016_s07
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx

value: NDN


title: DBL2

description: Pair-end, non-stranded

value: GV oocyte


title: NDN_ctrl_02 [RNA-seq]

description:
R02
Exp ID: 161229_0016_s02
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample21_603268: D00000000205641_WEEK 4_Etanercept

tag: plate


title: NDN_ctrl_01 [RNA-seq]

description:
R01
Exp ID: 170208_0025_s01
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx


title: Sample30_599106: D00000000205582_WEEK 4_Tofacitinib


title: Sample35_606964: D00000000205813_WEEK 4_Etanercept


title: FetalTreg4

city: San Francisco

first: Melissa

last: Ng

state: California

address: 35 Medical Centre Way, Regeneration Medicine Building 903B

institute: University of California, San Francisco

data_processing:
Fastq files were mapped to the genome using Bowtie 2
Read counts per gene was obtained using RSEM
TMM normalization and differential expression analysis performed using EdgeR package for Bioconductor
Genome_build: hg19
Supplementary_files_format_and_content: TMM-normalized data.

source_name: Fetal spleenocytes

extract_protocol:
Cells were sorted by FACS, and total RNA was extracted from 250,000 cells using the Nucleospin RNA kit (Machery Nagel)
Libraries were constructed using a standard Illumina protocol

value: fetal Treg cells

value: Fetal spleenocytes

value: 23.0 weeks

tag: Sex

value: Male


title: Col5

city: Guangzhou

first: Yuxia

last: Zhang

address: Jinsui Road

department: Guangzhou Institute of Pediatrics

country: China

institute: Guangzhou Women and Children's Medical Center, Guangzhou Medical University

description: Single cell 5' expression library

data_processing:
Samples were demultiplexed using Illumina bcl2fasq software
The Cell Ranger v2.1.1 pipeline (10x Genomics) was utilized to align reads to the transcriptome and summarize counts
The unique molecular identifier (UMI) count matrix was converted to a Seurat object using the R package Seurat v2.3.4. During this process, only cells with at least 200 genes detected and genes expressed in at least 3 cells were retained. The raw UMI counts matrix was then normalized using the Seurat’s NormalizeData function, in which the number of UMIs of each gene was divided by the sum of total UMIs per cell and multiplied by 10000, then transformed to log-scale (In(UMI-per-10000+1)).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited raw gene expression matrix (UMI counts)
Supplementary_files_format_and_content: tab-delimited normalized gene expression matrix (In(UMIs-per-10000+1))

source_name: colon

extract_protocol:
Single-cell suspensions were obtained by digestion with collagenase 1A (1 mg/mL) and DNase I (10 U/mL) with gentle rotation at 37ºC for 30 minutes, stained with antibodies (CD45-APC-Cy7, CD3-FITC, CD19-APC) in PBS solution supplemented with 2% FBS and 1 mM EDTA, and sorted by FACSAria SORP flow cytometry (BD Science) into 1% FBS pre-treated Eppendorf tubes. Based on different objectives, sorted cells were subjected to library constructions for transcriptome.
Single-cell suspension was mixed with RT-PCR master mix and loaded with nanoliter-scale Gel Beads and Partitioning Oil into a Single Cell 5’ Chip according to the manufacturer’s instructions. RNA transcripts from single cells were uniquely barcoded. After reverse transcription, barcoded cDNAs were purified, amplified, end-repaired, and ligated with Illumina adapters as per the manufacturer’s protocol to generate a single multiplexed library. The TCR or BCR libraries were amplified from the cDNA according to the manufacturer’s instructions included with the Chromium Single Cell V(D)J Enrichment Kit for human T cells or B cells.

tag: patient origin

tag: marker


title: Col6

description: Single cell 3' expression library


title: Sample19_602790: D00000000205667_WEEK 4_Etanercept

value: Etanercept 50 mg BIW


title: FetalTreg3


title: Sample34_602812: D00000000205575_WEEK 4_Etanercept


title: Sample18_607188: D00000000205617_WEEK 4_Etanercept


title: NDN_ctrl_04 [RNA-seq]

description:
R04
Exp ID: 161229_0016_s08
mRNA
processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx

value: Healthy (control)


title: Col4

description: Single cell 5' expression library


title: Sample27_602100: D00000000205750_WEEK 4_Tofacitinib


title: FetalTreg2

value: 22.2 weeks

value: Not determined


title: Sample26_595758: D00000000205775_DAY 1_Tofacitinib

value: DAY 1


title: Sample17_600418: D00000000205594_DAY 1_Tofacitinib

value: R


title: Col3

description: Single cell 5' expression library


title: FetalTreg1

value: 21.1 weeks


title: Col2

description: Single cell 5' expression library


title: Sample16_607214: D00000000205585_DAY 1_Etanercept


title: Sample25_597338: D00000000205741_DAY 1_Etanercept


title: Sample29_599194: D00000000205587_WEEK 4_Tofacitinib

value: WEEK 4

value: Tofacitinib

value: M


title: Sample23_599132: D00000000205801_WEEK 4_Tofacitinib


title: Col1

description: Single cell 5' expression library


title: Sample15_597688: D00000000205732_DAY 1_Tofacitinib


title: Sample20_597870: D00000000205726_DAY 1_Etanercept

value: Etanercept

value: NR

value: F


title: FetalNaive4

value: fetal naive T cells


title: FetalNaive3

value: Fetal spleenocytes


title: Sample22_603268: D00000000205641_WEEK 4_Etanercept


title: S280

description:
Single cell 3' expression library
processed data files:
S279_S280_3prime_raw_gene_expression.txt.gz
S279_S280_3prime_normalized_gene_expression.txt.gz
column headers for this sample are identified with the barcode sequence followed by "-2"

data_processing:
Samples were demultiplexed using Illumina bcl2fasq software
R1 contains the cell barcode (bp 1-16) and UMI (bp 17-26); R2 is the biological read
The Cell Ranger v2.1.1 pipeline (10x Genomics) was utilized to align reads to the transcriptome and summarize counts
The unique molecular identifier (UMI) count matrix was converted to a Seurat object using the R package Seurat v2.3.4. During this process, only cells with at least 200 genes detected and genes expressed in at least 3 cells were retained. The raw UMI counts matrix was then normalized using the Seurat’s NormalizeData function, in which the number of UMIs of each gene was divided by the sum of total UMIs per cell and multiplied by 10000, then transformed to log-scale (In(UMI-per-10000+1)).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited raw gene expression matrix (UMI counts)
Supplementary_files_format_and_content: tab-delimited normalized gene expression matrix (In(UMIs-per-10000+1))

extract_protocol:
Single cell suspension was obtained by digestion with gentle rotation at 37℃ for 30 minutes with collagenase 1A (1 mg/mL) and DNase I (10 U/mL), stained with antibodies CD19-APC, CD45-APC-cy7, CD3-FITC in PBS (with 2% FBS and 1mM EDTA), and sorted by FACS Aria Sorp flow cytometry (BD science) into 1% FBS pre-treated Eppendorf tubes. Based on different objectives, sorted cells were subjected to library constructions for transcriptome.
Single cell solution (viability >90%, 1000 cells/uL) was prepared and partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs). This would result with expected mRNA barcoding for ~5000 single-cells and multiplet rate of ~3.9%. After reverse transcription, GEMs were broken and barcoded-cDNA purified with Silane magnetic beads and Solid Phase Reversible Immobilization (SPRI) beads. Barcoded-cDNA was amplified by PCR (98ºC for 45s; [98ºC for 20s, 67ºC for 30s, 72ºC for 1 min] x 14; 72ºC for 1 min). For HB1, HB2, HB3-1, HB3-2 and HB4, the cDNA was subjected to library construction according to the instructions of Chromium Single Cell 5' library. For S279 and S280, the cDNA was subjected to library construction according to the instructions of Chromium Single Cell 3' library.

tag: cell markers

value: colon

tag: patient diagnosis

value: paediatric onset inflammatory bowel disease (PIBD)


title: S279

description:
Single cell 3' expression library
processed data files:
S279_S280_3prime_raw_gene_expression.txt.gz
S279_S280_3prime_normalized_gene_expression.txt.gz
column headers for this sample are identified with the barcode sequence followed by "-1"

tag: tissue


title: FetalNaive2

tag: cell type


title: Sample13_596414: D00000000205699_DAY 1_Tofacitinib


title: Sample21_597870: D00000000205726_DAY 1_Etanercept

value: Etanercept 50 mg BIW


title: Sample28_600672: D00000000205701_WEEK 4_Tofacitinib


title: HB4

description:
Single cell 5' expression library
processed data files:
HB1-4_5prime_raw_gene_expression.txt.gz
HB1-4_5prime_normalized_gene_expression.txt.gz
column headers for this sample are identified with the barcode sequence followed by "-5"


title: HB3-2

description:
Single cell 5' expression library
processed data files:
HB1-4_5prime_raw_gene_expression.txt.gz
HB1-4_5prime_normalized_gene_expression.txt.gz
column headers for this sample are identified with the barcode sequence followed by "-3"


title: Sample12_598844: D00000000205701_DAY 1_Tofacitinib


title: AdultTreg4

source_name: Human PBMCs

value: adult CD4+CD25hiCD127lo Treg cells

value: Human PBMCs

value: 70 years

value: Male


title: Sample20_602790: D00000000205667_WEEK 4_Etanercept


title: Sample11_602142: D00000000205771_DAY 1_Tofacitinib

value: DAY 1

value: R


title: FetalNaive1

value: 21.1 weeks

value: Not determined


title: Sample19_607188: D00000000205617_WEEK 4_Etanercept

value: WEEK 4

value: M


title: HB3-1

description:
Single cell 5' expression library
processed data files:
HB1-4_5prime_raw_gene_expression.txt.gz
HB1-4_5prime_normalized_gene_expression.txt.gz
column headers for this sample are identified with the barcode sequence followed by "-4"


title: Sample10_602084: D00000000205587_DAY 1_Tofacitinib

value: Tofacitinib


title: AdultTreg2

value: 35 years


title: HB2

description:
Single cell 5' expression library
processed data files:
HB1-4_5prime_raw_gene_expression.txt.gz
HB1-4_5prime_normalized_gene_expression.txt.gz
column headers for this sample are identified with the barcode sequence followed by "-2"


title: Sample17_607214: D00000000205585_DAY 1_Etanercept

value: Etanercept

value: NR

value: F


title: AdultTreg1

value: 26 years


title: HB1

description:
Single cell 5' expression library
processed data files:
HB1-4_5prime_raw_gene_expression.txt.gz
HB1-4_5prime_normalized_gene_expression.txt.gz
column headers for this sample are identified with the barcode sequence followed by "-1"

value: colon

value: paediatric onset inflammatory bowel disease (PIBD)


title: Sample9_606996: D00000000205723_DAY 1_Etanercept

value: Etanercept 50 mg BIW


title: Sample14_610108: D00000000205749_DAY 1_Tofacitinib


title: AdultNaive4

value: adult CD4+CD25-CD45RA+CD27+ naive T cells

value: Human PBMCs

value: 70 years


title: Sample16_597688: D00000000205732_DAY 1_Tofacitinib

value: DAY 1

value: R


title: Sample15_610108: D00000000205749_DAY 1_Tofacitinib


title: Sample8_598830: D00000000205582_DAY 1_Tofacitinib


title: AdultNaive3

value: 50 years

value: Male


title: Myoblast_Treated_10_S2

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

country: Spain

institute: Universidad de Valencia

data_processing:
Quality control was performed with FASTQC (version 0.11.8)
Aligment was performed with STAR (version 2.6.1a_08-27)
Gene counts were performed using featureCounts (1.6.3)
Isoforms counts were performed with using RSEM (1.3.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: gene counts, isoform counts

source_name: Myoblast

extract_protocol:
Tissues were homogenized using TissueLyser LT in TriReagent. Total RNA from human myoblasts was isolated using TriReagent following manufacturer’s recommendations. One microgram of RNA was digested with DNaseI and reverse-transcribed with SuperScript II Reverse Transcriptase using random hexanucleotides.
Library preparation was performed using TruSeq Stranded mRNA Library prep kit from Illumina without any change

value: DM1 (iPDF) skin fibroblasts transdifferentiated into myoblast

value: chloroquine at 10M


title: Myoblast_Treated_10_S3


title: Sample14_596414: D00000000205699_DAY 1_Tofacitinib

value: Tofacitinib


title: AdultTreg3

value: adult CD4+CD25hiCD127lo Treg cells


title: AdultNaive2

value: 35 years


title: AdultNaive1


title: Myoblast_Treated_10_S1


title: Sample13_598844: D00000000205701_DAY 1_Tofacitinib

value: NR

value: F


title: Sample18_600418: D00000000205594_DAY 1_Tofacitinib

value: M


title: Sample7_607504: D00000000205679_WEEK 4_Tofacitinib

value: WEEK 4


title: Myoblast_Treated_01_S3

value: chloroquine at 0.1M


title: Sample4_598932: D00000000205693_DAY 1_Etanercept

value: Etanercept 50 mg BIW

value: Etanercept


title: Myoblast_Treated_01_S2


title: Sample6_601626: D00000000205654_DAY 1_Tofacitinib


title: Sample5_596526: D00000000205667_DAY 1_Etanercept


title: Sample3_589174: D00000000205719_DAY 1_Tofacitinib


title: Myoblast_Treated_01_S1


title: Sample2_607608: D00000000205723_WEEK 4_Etanercept


title: Myoblast_Disease3


title: NPRA +/+,242

city: 西安

first: Jun

last: Yu

state: Shaanxi

address: North of Wei 32nd Road, and east of Xitai Road, High-tech Zone

department: Clinical Experimental Center

institute: Xi'an International Medical Center Hospital

description:
242
circRNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software (version 11.0.1.1). A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 4 out of 8 samples have flags in P or M (“All Targets Value”) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: NPRA+/+ myocardium

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

growth_protocol: Myocardium tissue from cardiac-specific NPRA-deficient mice and normal mice.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from myocardium were immersed overnight in RNAlater at 4 ℃ and preserved at -80 ℃.

tag: strain/background

tag: genotype/variation

value: wild type

value: myocardium


tag: visit

value: DAY 1

tag: treatment


tag: treatmentshort

tag: pasi

value: R


title: Sample1_601846: D00000000205759_WEEK 4_Tofacitinib

tag: tag

tag: age


title: Myoblast_Disease2


title: NPRA +/+,230

description:
230
circRNA


title: Myoblast_Disease1


title: Myoblast_Control3

value: normal (iCDF) skin fibroblasts transdifferentiated into myoblast


title: Sample10_602084: D00000000205587_DAY 1_Tofacitinib

tag: gender

tag: platesimple


tag: plate


title: NPRA +/+,228

description:
228
circRNA


title: ΔgdhR/pGCC4-gdhR rep2

city: Atlanta

first: Julio

middle: C.

last: Ayala

state: Georgia

address: 1600 Clifton Rd NE Rm 3-642

department: Division of STD Prevention

institute: Centers for Disease Control and Prevention

description:
processed data files:
Table-2. Genes differentially expressed between gdhR mutant and complemented strain.xlsx

data_processing:
Base call (BCL) files generated by the sequencing platform were converted to FASTQ using the Illumina cloud service BaseSpace Sequence Hub.
Paired-end sequencing FASTQ files were aligned to the N. gonorrhoeae FA19 genome by using the Tophat2 algorithm (available at the public ABIMS Galaxy tool shed from the Station Biologique de Roscoff-CNRS-Sorbonne University) to generate BAM files. With parameters: Use gene annotation file (yes); Use own junctions (yes).
Cuffdiff algorithm (available at the ABIMS Galaxy server) was used to determined transcript differential expression reports between strains using duplicate samples per analyzed condition. With parameters: Transcripts (FA19 genome .gff annotation file); Library normalization method (classic-fpkm); Reference sequence data (FA19 genome .fna file); Set additional parameters (No).
Genome_build: N. gonorrhoeae FA19 strain with GenBank assembly accession number GCA_000273665.1
Supplementary_files_format_and_content: .xlsx files consisting of the transcript differential expression Cuffdiff report for each comparison and containing the FPKM expression values for each sample, mutant to WT fold-change ratios, statistical significance, etc. Text files describing the alignment rate results of the FASTQ files after Tophat2 software processing.

organism: Neisseria gonorrhoeae

source_name: GC broth-grown planktonic cells

growth_protocol: N. gonorrhoeae strains were grown in 25 mL GC broth with Kellogg’s supplements I and II and 0.042% NaHCO3 at 37°C under 5% (v/v) CO2 with agitation (225 rpm) to optical densities at 600 nm (OD600) of approximately 1.0. Complemented gdhR mutants expressing gdhR from the lac promoter were added 1 mM IPTG for protein expression induction.

extract_protocol:
Total RNA extraction was conducted using the RNeasy mini kit (Qiagen), following the manufacturer’s protocol. One hundred µL of 200 ng/µL total isolated RNA were treated to remove genomic DNA contamination using the Turbo DNA-free Kit (Invitrogen) as per the manufacturer’s instructions. One hundred µL of DNase I-digested total RNA samples were concentrated and cleaned-up using the RNeasy MinElute Cleanup Kit (QIAGEN). Finally samples were eluted from the RNeasy MinElute spin columns with 24 µL of Nuclease-Free water (Ambion) and stored at -80 °C until library preparation.
RNA-sequencing was performed on the Illumina NextSeq 500 as described by the manufacturer (Illumina Inc., San Diego, CA). The quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer.  RNA with a RNA Integrity Number (RIN) of 7.0 or above was used for sequencing library preparation. Library preparation was done using the Agilent SureSelect Strand Specific mRNA library kit as per the manufacturer’s instructions (Agilent, Santa Clara, CA).  Library construction began with ribosome reduction using the RiboMinus rRNA depletion kit for bacteria (Invitrogen). The resulting RNA was randomly fragmented with cations and heat, which was followed by first strand synthesis using random primers with inclusion of Actinomycin D (2.4ng/µL final concentration).  Second strand cDNA production was done with standard techniques, the ends of the resulting cDNA were made blunt, A-tailed and adaptors ligated for amplification and indexing to allow for multiplexing during sequencing.  The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.  Cluster generation was performed according to the manufacturer’s recommendations for onboard clustering (Illumina).

treatment_protocol: One mL samples collected at OD600 1.0 were centrifuged for 2 min at 10000 g and 4°C, resuspended in 200 µL RNAlater solution (Ambion) and incubated 10 min on ice. Then, samples were centrifuged 3 min at 6500 g and 4°C and the pellets were stored at -80 °C for RNA extraction.

tag: strain

value: FA19 StrR

tag: genotype

value: gdhR::Km complemented in trans


title: ΔgdhR/pGCC4-gdhR rep1


title: ΔgdhR rep2

description:
processed data files:
Table-1. Genes differentially expressed between Wt and gdhR mutant.xlsx
Table-2. Genes differentially expressed between gdhR mutant and complemented strain.xlsx


title: ΔgdhR rep1


title: WT rep2

description:
processed data files:
Table-1. Genes differentially expressed between Wt and gdhR mutant.xlsx

value: WT


title: Myoblast_Control1


title: Myoblast_Control2


value: Tofacitinib


title: NPRA -/-,231

description:
231
circRNA

source_name: NPRA-/- myocardium

value: NPRA-/-


title: WT rep1


title: NPRA -/-,241

description:
241
circRNA


title: NPRA -/-,240

description:
240
circRNA


title: NPRA -/-,227

description:
227
circRNA


title: NPRA -/-,217

description:
217
circRNA


title: FSW.020

status: Public on Nov 21 2019

first: Louise

middle: C

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

description: SAMPLE 18

hyb_protocol: Standard Illumina DASL hybridization protocol

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis.

label: biotin

source_name: Ectoservical biopsy, female sex worker

label_protocol: Standard Illumina DASL label protocol

extract_protocol: Total RNA from formalin-fixed paraffin embedded tissues was isolated with High Pure RNA Paraffin Kit (Roche Applied Science, Branford, CT).

treatment_protocol: Ectocervical biopsies were placed in Safe Fix II All-Purpose Fixative (Fisher) for 4 hours at room temperature, and then washed twice in 80% ethanol (5 minutes) and then stored in 80% ethanol (room temperature) until embedded in paraffin.

tag: individual

value: HIV resistant sex worker

value: ectocervical biopsy


title: FSW.007

description: SAMPLE 13


title: FSW.006

description: SAMPLE 12


title: FSW.027

description: SAMPLE 16


title: FSW.067

description: SAMPLE 22


title: brat RNAi numb RNAi neuroblasts replicate 1 (input H3K27me3)

city: Vienna

first: Merve

middle: Deniz

last: Abdusselamoglu

address: Doktor. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)

description: brat-numb-SBa67-H3K27me3.subtractInput.bw

library_source: genomic

data_processing:
Reads are aligned to dm3 with bowtie2 (v2.2.4).
Coverage tracks are produced with deeptools (v2.5.0.1) by subtracting the respective input (--ratio subtract --normalizeTo1x 121400000 -bs 1).
Reads of ChIP alignments are counted with multiBamCov of bedtools (v2.25.0). H3K4me3 reads are counted in a 500bp region downstream of the first TSS. H3K27me3 reads are counted over the genebody. Flybase 5.44 is used as annotation.
Genome_build: dm3
Supplementary_files_format_and_content: bigwig (coverage subtracted by input); txt (read counts in region)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: neural stem cells

growth_protocol: Larvae were reared on standard fly food until L3 stage (wandering).

extract_protocol:
NBs and neurons were isolated according to Harzer et. Al (2013, Nature protocols). Samples were MNase treated.
Libraries were prepared according to Bowman et. Al (2013 BMC Genomics).

value: tumor neuroblasts

value: L3 larval brain


title: brat RNAi neuroblasts replicate 2 (input H3K4me3/H3K27me3)

description:
brat-SBa68-H3K4me3.subtractInput.bw
brat-SBa68-H3K27me3.subtractInput.bw


title: neurons replicate 1 (input H3K27me3)

source_name: neurons

value: neurons


title: brat RNAi numb RNAi neuroblasts replicate 2 (input H3K4me3/H3K27me3)

description:
brat-numb-SBa68-H3K4me3.subtractInput.bw
brat-numb-SBa68-H3K27me3.subtractInput.bw


title: neurons replicate 2 (input H3K27me3)


title: type I neuroblasts replicate 2 (input H3K27me3)

value: neuroblasts


title: brat RNAi neuroblasts replicate 1 (input H3K27me3)


title: CG.110

description: SAMPLE 5

source_name: Ectocervical biopsy, control group

value: control


title: CG.114

description: SAMPLE 9


title: FSW.050

description: SAMPLE 20


title: CG.058

description: SAMPLE 2


title: CG.113

description: SAMPLE 8


title: FSW.003

description: SAMPLE 11


title: FSW.075

description: SAMPLE 23


title: FSW.016

description: SAMPLE 15


title: FSW.002

description: SAMPLE 10


title: FSW.035

description: SAMPLE 17


title: CG.112

description: SAMPLE 7


title: CG.111

description: SAMPLE 6


title: CG.055

description: SAMPLE 1


title: CG.103

description: SAMPLE 4


title: CG.088

description: SAMPLE 3


title: FSW.026

description: SAMPLE 19


title: FSW.013

description: SAMPLE 14


title: FSW.059

description: SAMPLE 21


title: type I neuroblasts replicate 1 (input H3K27me3)


title: neurons replicate 2 (input H3K4me3)


title: brat RNAi neuroblasts replicate 1 (input H3K4me3)


title: type I neuroblasts replicate 2 (input H3K4me3)


title: brat RNAi neuroblasts replicate 2 (H3K27me3)

tag: chip antibody

value: H3K27me3 (Active Motif 39155)


title: brat RNAi numb RNAi neuroblasts replicate 1 (input H3K4me3)

description: brat-numb-SBa67-H3K4me3.subtractInput.bw

tag: tissue


title: neurons replicate 2 (H3K27me3)

tag: cell type


title: brat RNAi numb RNAi neuroblasts replicate 2 (H3K27me3)

description: brat-numb-SBa68-H3K27me3.subtractInput.bw


title: neurons replicate 1 (input H3K4me3)


title: brat RNAi numb RNAi neuroblasts replicate 1 (H3K27me3)


title: neurons replicate 1 (H3K27me3)


title: type I neuroblasts replicate 1 (H3K27me3)


title: type I neuroblasts replicate 1 (input H3K4me3)


title: neurons replicate 2 (H3K4me3)

value: H3K4me3 (Millipore 07-473)


title: neurons replicate 1 (H3K4me3)


title: type I neuroblasts replicate 2 (H3K4me3)


title: brat RNAi neuroblasts replicate 1 (H3K4me3)


title: brat RNAi numb RNAi neuroblasts replicate 2 (H3K4me3)

description: brat-numb-SBa68-H3K4me3.subtractInput.bw


title: type I neuroblasts replicate 1 (H3K4me3)


title: brat RNAi neuroblasts replicate 1 (H3K27me3)


title: 7A_c

city: Bandung

first: Fenny

last: Dwivany

address: Jl. Ganesha No. 10

country: Indonesia

institute: Institut Teknologi Bandung

description:
replicate 3
Musa acuminata (AAA Group, Subgroup Cavendish)

data_processing:
Raw paired-end reads were examined for a possible low base score, Illumina adapter, and PCR contaminations using FastQC
Clean reads were mapped against genome reference using TopHat-Cufflink pipeline (Trapnell et al. 2012)
Reads that aligned to annotated loci were quantified and normalized with FPKM value using Cufflinks V2.2.2.1 (Trapnell et al. 2012)
Genome_build: Musa acuminata DH Pahang V2 (available at https://banana-genome-hub.southgreen.fr)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Musa acuminata AAA Group

source_name: fruit pulp

extract_protocol:
Total RNA were extracted from the fruit pulp using RNA isolation method according to Cordeiro et al. (2008)
RNA libraries were prepared for sequencing using standars Ilumina protocols

treatment_protocol: Banana fruit was treated in two conditions, i.e. control and chitosan-coated. Controls are fruits without chitosan coating. Chitosan-coated are fruits with chitosan coating, the fruits were dipped in 1.25% chitosan solution for coating process.

tag: developmental stage

value: Day 7 of fruit ripening

value: 1.25percent chitosan-coated fruit

value: fruit pulp


title: brat RNAi neuroblasts replicate 2 (H3K4me3)


title: 7A_b

description:
replicate 2
Musa acuminata (AAA Group, Subgroup Cavendish)


title: type I neuroblasts replicate 2 (H3K27me3)


title: 7K_c

value: Control (uncoated)


title: 7A_a

description:
replicate 1
Musa acuminata (AAA Group, Subgroup Cavendish)


title: 7K_a


title: 7K_b


title: 1A_c

value: Day 1 of fruit ripening


title: brat RNAi numb RNAi neuroblasts replicate 1 (H3K4me3)


title: 1A_b


title: 1A_a


title: 1K_b


title: 1K_a


title: RPL30_RSC_RAP1

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description: PCR generated DNA fragment

data_processing:
For MNase-Seq, mapping of the sequencing data to the corresponding sequences was performed using Bowtie2 (sensitive end-to-end mode) on Galaxy (https://usegalaxy.org/).  All densities were derived from read counts normalized to the total number of reads for each sample and BAM files was converted to bigWig files using bamCoverage and bigWig files converted to BedGraph format on Galaxy
genome_build: FASTA files used for read alignment are available on the series record.
Supplementary_files_format_and_content: BAM files was converted to bigWig files using bamCoverage and bigWig files converted to BedGraph format on Galaxy

organism: synthetic construct

source_name: with RSC and RAP1

extract_protocol:
RSC sliding reactions were performed in reaction buffer (10mM Tris pH7.4, 150mM KCl, 3mM MgCl2, 0.1mg/ml BSA) and a total volume of 70µl. The following components were added in sequential order mononucleosomes (to make 20nM final concentration), Nap1 (10 Nap1 : 1 mononucleosome ratio), Rap1 (10 Rap1 : 1 mononucleosome ratio, for w/o Rap1 MQ water was used as substitute), RSC complex (1 RSC : 5 mononucleosome ratio) and finally ATP (1mM). Reactions were placed at 30°C for 90 mins after which 10ul was taken and glucose was added to make 8% final concentration and loaded onto commercial Criterion Precast Gel (Biorad) 5% acrylamide, 1mm, run in 1xTBE at 200V for 35-45mins on ice. Gels were stained in Gelred and imaged using ChemiDoc MP (Biorad). To the remaining 60ul, 60ul 50mM Tris-HCl pH 8 and 10x NEB MNase buffer (M0247S) (to make final 1x) was added. This 120ul total sample was split into 3 x 40ul aliquots and to each either 6 units, 3 units or 1 unit of Mnase (M0247S) was added respectively and left to digest for 5 mins at 37° C. To stop the reaction an equal volume of stop buffer was added (200mM NaCl, 30mM EDTA, 1% SDS) and left on ice for 5 mins. Finally, 10µg of Proteinase K (Sigma P2308) was added and left for 1h at 60° C and DNA fragments were isolated using QIAquick PCR purification spin columns (Qiagen). For nucleosome only samples (t0), reactions were performed directly in 1x NEB Mnase buffer (M0247S), Mnase and Proteinase K digestion as well as DNA fragment purification was performed as described for RSC assay nucleosomes. All purified samples, were run on a 2% agarose 1xTBE gels for run in 1xTBE at 110V for 60min. Gels were stained in Gelred and imaged using ChemiDoc MP (Biorad).
TruSeq ChIP library preparation kit (Illumina)

treatment_protocol: with RSC and RAP1

tag: dna source

value: Plasmids containing recombinant DNA fragments (Kilic et al., 2018)

tag: nucleosome type


title: sample_050

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Breast cancer cells treated by the antimitotic Paclitaxel

hyb_protocol: Double-stranded complementary DNA (cDNA) and labeled complementary RNA (cRNA) were synthesized from the total RNA and hybridized to the Affymetrix Human U133 Plus 2 gene chips (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were further processed and scanned according to the manufacturer’s protocol using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

label_protocol: According to manufacturer protocol.

growth_protocol: Cells lines were purchased from ATCC and cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Saint Aubin, France) supplemented with 2 mM glutamine and 1% penicillin/streptomycin (Gibco) and 5% Fetal Bovine Serum (FBS) (Eurobio, Courtaboeuf, France).

extract_protocol: Total RNA was prepared using the RNeasy® Mini kit (Qiagen, Valencia, CA). The integrity of the RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: 3.5 nM Paclitaxel (Sigma-Aldrich, St Quentin Fallavier, France)

value: Breast cancer cells

tag: sensitivity to bcl-xl inhibition

value: Resistant


title: sample_060

source_name: Breast cancer cells treated by the antimitotic Paclitaxel


title: sample_048


title: sample_055


title: sample_058


title: sample_047

value: Sensitive


title: sample_054


title: 1K_c

tag: treatment


title: sample_046


title: RPL30_RSC

description: PCR generated DNA fragment

source_name: with RSC/ no RAP1

treatment_protocol: with RSC/ no RAP1


title: sample_057


title: sample_043


title: 601_S1S2_RSC_RAP1

description: PCR generated DNA fragment


title: 601_S1S2_RSC

description: PCR generated DNA fragment


title: sample_044


title: sample_051


title: sample_056


title: sample_053


title: sample_049


title: sample_059


title: 601_S1S2

description: PCR generated DNA fragment

source_name: no RSC/ no RAP1

treatment_protocol: no RSC/ no RAP1


title: Bb768_10-28_2012

city: Zhoushan

first: Jianhua

last: Liu

state: Zhejiang

address: 10 Tiyu Road, Room 502

department: Ocean Research Centre of Zhoushan

institute: Zhejiang University

data_processing:
Using FastQC to check the qualities of sequenced reads
De novo assembly using Trinity with processed reads (ALL biosamples) (--CPU 7 --min_contig_length 300 --KMER_SIZE 25)
Transcriptome were annotated by running BLASTX to 6 algal genomes (evalue < 1e-7, length of homology to subject/ full length> 25%) (-max_target_seqs 1 -num_threads 60 -outfmt 6 -evalue 1e-7)
Expression levels of annotated EST were determined using Trinity-bundled perl script align_and_estimate_abundance.pl which utilizes RSEM to calculate FPKM values (--est_method RSEM --aln_method bowtie2 --thread_count 7 --trinity_mode)
Supplementary_files_format_and_content: abundance measurements Matrix containing TPMs
Supplementary_files_format_and_content: Non-redundant assembly of B.braunii AC768: Bb768_NR_48767.fa
Supplementary_files_format_and_content: FASTA sequences with annotation in this study: Bb768_annotated_5980.fa

organism: Botryococcus braunii

source_name: AC768 algae culture cells

extract_protocol:
Total RNA from B.braunii AC768 cells was isolated using RNeasy Plant Mini Kit (Qiagen, Netherlands) according to the manufacturer’s instructions. RNA integrity number (RIN) was measured using RNA 6000 Pico Kit (Agilent, USA) on an Agilent 2100 Bioanalyzer (Schroeder et al., 2006).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RPL30

description: PCR generated DNA fragment


title: sample_042


title: sample_045


title: sample_040


title: KO_RNase_Riboseq_rep1

city: Beijing

first: Jinghui

last: Song

address: 5 Yiheyuan Road, Haidian District

institute: Peking university

data_processing:
Library strategy: Ribo-seq
Basecalls performed using Illumina CASAVA.
For reads cleanning, adaptor were trimmed and low quality reads were filtered with Trim_galore software (version: 0.3.3).
Cleaned reads were mapped to reference genome (hg19 and genomic tRNA database [GtRNAdb (http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi19/)]) using TopHat version 2.1.0 (rRNA(-) nuclear RNA-seq and polyA RNA-seq) and Bowtie version 1.2.2 (PAR-CLIP-seq and DM-Ψ-seq).
Abundance measurements were performed by Cufflinkes version 2.2.1 (polyA RNA-seq) and Htseq-count version 0.9.1 (rRNA(-) nuclear RNA-seq). Peak-calling of PAR-CLIP were performed by PARalyzer version 1.5. Site-calling of DM-Ψ-seq were performed by custom scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Codon_Occupancy.tar
Supplementary_files_format_and_content: MNase_TE.txt

growth_protocol: HEK293T cells were maintained at 37 °C in DMEM medium (Corning) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
For rRNA(-) nuclear RNA-seq, cell fractionation was performed, and the resulting RNA was subjected to two rounds of rRNA removal using RiboMinus™ Eukaryote Kit for RNA-Seq .For polyA RNA-seq, total RNA was isolated from cell lines with Trizol (invitrogen) according to the manufacturer’s instructions. Two rounds of poly-A selection were performed using Dynabeads™ Oligo(dT)25 (Invitrogen) to obtain mRNA. For PAR-CLIP-seq, five 15 cm dishes of HEK293T cells were transfected with flag-tagged PUS10 plasmid at 80% confluency. After 6 h, the media was changed and 200 μM 4SU was added. After additional 18 h, the cells were washed once with 10 ml ice-cold PBS for each plate. Then, the plates were kept on ice, and the UV crosslink was carried out twice by 150 mJ/cm2 at 365 nm. After immunoprecipitation,  the final recovered RNA sample was further cleaned by RNA Clean & Concentrator (Zymo Research). For DM-Ψ-seq, small RNA (<200 nt) was isolated and purified from cell culture using miRNeasy Mini Kit, RNeasy MinElute Cleanup Kit and RNase-free DNase Set (Qiagen) according to the manufacturer’s instructions.
The rRNA(-) nuclear RNA and poly-A RNA were used to construct RNA-seq library under the instruction of NEBNext® Ultra™ RNA Library Prep Kit for Illumina. For PAR-CLIP-seq, the RNA samples were used to construct library under the instruction of NEBNext® Multiplex Small RNA Library Prep Set for Illumina. For DM-Ψ-seq,  the library construction was performed according to the eCLIP library construction protocol with several modifications.

treatment_protocol: For cell passage, cells were first washed with PBS. Trypsin was added to the dishes, which were then incubate at 37 °C for 2-5 min, and FBS containing medium was used to inactive trypsin. After collected by centrifuge at 1000 g for 3 min, cells were counted and split for different purposes. Generation of PUS10 knockout HEK293T cells was achieved by using CRISPR/Cas9 technology.

tag: cell line

tag: molecule subtype

value: Ribosome protected RNA


title: KO_MNase_Riboseq_rep2


title: KO_RNase_Riboseq_Input_rep2

value: total RNA input


title: KO_RNase_Riboseq_rep2


title: KO_RNase_Riboseq_Input_rep1


title: KO_MNase_Riboseq_rep1


title: KO_MNase_Riboseq_Input_rep1


title: WT_RNase_Riboseq_rep2

value: WT


title: KO_MNase_Riboseq_Input_rep2


title: sample_039


title: WT_RNase_Riboseq_Input_rep2


title: WT_RNase_Riboseq_rep1


title: sample_038


title: sample_037


title: sample_032


title: sample_041


title: sample_033


title: WT_RNase_Riboseq_Input_rep1


title: sample_035


title: sample_031


title: WT_MNase_Riboseq_rep2


title: sample_036


title: sample_052


title: sample_030


title: sample_029


title: sample_027


title: WT_MNase_Riboseq_Input_rep2


title: WT_MNase_Riboseq_rep1


title: WT_MNase_Riboseq_Input_rep1


title: sample_026


title: sample_025


title: WT_CMC_Rep3

description:
small RNA
processed data file:
DM_psiU_seq_WT_sites.txt
Libraries were sequenced with paired-end strategy but due to the particularity of our library construction (a random barcode of 10 nt were included in our 3' end cDNA adapter, which cannot be precisely located in Read 1), data of Read 1 were discarded and only the data of Read 2 were used in our analysis. Only Read 2 was submitted.

data_processing:
Library strategy: DM-psiU-seq
Basecalls performed using Illumina CASAVA.
For reads cleanning, adaptor were trimmed and low quality reads were filtered with Trim_galore software (version: 0.3.3).
Cleaned reads were mapped to reference genome (hg19 and genomic tRNA database [GtRNAdb (http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi19/)]) using TopHat version 2.1.0 (rRNA(-) nuclear RNA-seq and polyA RNA-seq) and Bowtie version 1.2.2 (PAR-CLIP-seq and DM-Ψ-seq).
Abundance measurements were performed by Cufflinks version 2.2.1 (polyA RNA-seq) and Htseq-count version 0.9.1 (rRNA(-) nuclear RNA-seq). Peak-calling of PAR-CLIP were performed by PARalyzer version 1.5. Site-calling of DM-Ψ-seq were performed by custom scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values, peak calling and site calling for each group of samples.


title: KO_BEU_Rep3

description:
small RNA
processed data file:
DM_psiU_seq_KO_sites.txt
Libraries were sequenced with paired-end strategy but due to the particularity of our library construction (a random barcode of 10 nt were included in our 3' end cDNA adapter, which cannot be precisely located in Read 1), data of Read 1 were discarded and only the data of Read 2 were used in our analysis. Only Read 2 was submitted.


title: KO_CMC_Rep1


title: KO_BEU_Rep2


title: sample_022


title: sample_021


title: sample_024


title: WT_CMC_Rep1


title: WT_CMC_Rep2


title: KO_CMC_Rep2


title: sample_020


title: WT_BEU_Rep1


title: sample_018


title: KO_CMC_Rep3


title: sample_017


title: KO_polyA_RNA_seq_Rep2

description:
polyA RNA
processed data file:
PolyA_RNA_seq_summary.txt

data_processing:
Basecalls performed using Illumina CASAVA.
For reads cleanning, adaptor were trimmed and low quality reads were filtered with Trim_galore software (version: 0.3.3).
Cleaned reads were mapped to reference genome (hg19 and genomic tRNA database [GtRNAdb (http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi19/)]) using TopHat version 2.1.0 (rRNA(-) nuclear RNA-seq and polyA RNA-seq) and Bowtie version 1.2.2 (PAR-CLIP-seq and DM-Ψ-seq).
Abundance measurements were performed by Cufflinks version 2.2.1 (polyA RNA-seq) and Htseq-count version 0.9.1 (rRNA(-) nuclear RNA-seq). Peak-calling of PAR-CLIP were performed by PARalyzer version 1.5. Site-calling of DM-Ψ-seq were performed by custom scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values, peak calling and site calling for each group of samples.


title: sample_023


title: sample_019


title: KO_polyA_RNA_seq_Rep1


title: sample_015


title: WT_BEU_Rep3


title: sample_014


title: sample_016


title: WT_BEU_Rep2


title: sample_010


title: sample_013


title: sample_009


title: WT_polyA_RNA_seq_Rep1


title: KO_rRNA(-)_nuclear_RNA_seq_Rep2

description:
rRNA(-) nuclear RNA
processed data file:
Nuclear_RNA_seq_summary.txt


title: KO_rRNA(-)_nuclear_RNA_seq_Rep1


title: sample_012


title: sample_011


title: sample_028


title: sample_008


title: sample_007


title: sample_034


title: WT_rRNA(-)_nuclear_RNA_seq_Rep2


title: WT_rRNA(-)_nuclear_RNA_seq_Rep1


title: sample_005


title: WT_polyA_RNA_seq_Rep2


title: sample_003


title: sample_004


title: N134_GFP-miR-431_7

first: Nancy

last: Du

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Illumina CASAVA v1.8.2 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the mouse mm9 reference genome using Tophat v2.0.11.
Differential expression analysis was performed by using Cufflinks v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: excel file including gene name, refseq gene id, expression (FPKM) for each gene in each sample

growth_protocol: cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 0.2 mM L-glutamine, and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Plus mini kit (Qiagen, 74134) and QIAshredder kit (Qiagen, 79654) according to the manufacturer’s protocol.
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced with pair-end 51 bps on Illumina HiSeq 4000 sequencer (Illumina, San Diego, CA).

value: pancreatic beta cell tumor

value: overexpressing GFP-miR-431


title: N134_GFP-miR-431_5


title: N134_GFP-miR-431_6


title: N134_GFP-miR-LacZ_4

value: control


title: N134_GFP-miR-LacZ_3


title: T1_E

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

description: multiple sub-samples (more information found in separete sample information file)

data_processing:
Sequencing in 75 cycles produced 20 bp Read 1 (bases 1-12 sample barcode, bases 13-20 UMI) and 55 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was filtered to remove reads shorter than 20 bp.
The original pipeline suggested in (Macosko EZ et al. Cell 2015; https://github.com/broadinstitute/Drop-seq) for processing of drop-seq data was used. Briefly, reads were additionally filtered to remove polyA tails of length 6 or greater, then aligned to the mouse (mm10) genome using STAR aligner, with default settings. Uniquely mapped reads were grouped according to the 1-12 barcode, and gene transcripts were counted by their Unique Molecular Identifiers (UMIs) to reduce bias emerging from the PCR amplification. Digital expression matrices (DGE) reported the number of transcripts per gene in a given sample (according to the distinct UMI sequences counted).
Differentially expressed genes were identified using edgeR
Supplementary_files_format_and_content: Digital Gene Expression (DGE): tab-delimited text file containing UMI read counts for each sample

source_name: spleen

growth_protocol: Spleen cells were treated with ACK buffer for 10 min for erythrocyte lysis. They were cultured in 24-well plates in complete RPMI 1640 medium (containing 10% FCS, penicillin/streptomycin, glutamine, 25mM Hepes buffer; 7.5 x 106 cells/well) for 72h at 37°C, 5% CO2.

extract_protocol:
RNA was extracted from mouse spleen cells using the RNeasy Mini Kit (Qiagen) and following manufacturer’s guidelines. Cells were homogenized with QIAshredder colums (Qiagen). DNA digestion was performed using RNase-free DNase (Qiagen). RNA integrity was assessed using the LabChip GXII Touch HT electrophoresis system, with the RNA Assay and the DNA 5K / RNA / Charge Variant Assay LabChip (all PerkinElmer). RNA samples were stored at -70°C.
RNA sequencing method was designed based on the Drop-seq protocol described in (Macosko EZ et al. Cell 2015). Briefly, 10 ng of RNA was mixed with Indexing Oligonucleotides. After 5 minutes of incubation the RNA was combined with RT mix (1 x Maxima RT buffer, 1 mM dNTPs, 10 U/µl Maxima H- RTase, 1 U/µl RNase inhibitor and 2.5 µM Template Switch Oligo). Samples were incubated for 30 minutes at 22°C and 90 minutes at 42°C. The constructed cDNA was amplified by PCR. The PCR products were pooled together in sets of 12 samples containing different Indexing Oligos and purified with Agencourt AMPure XP Beads according to the manufacturer’s instructions. The 3’-end cDNA fragments for sequencing were prepared using the Nextera XT (Illumina) tagmentation reaction. The reaction was performed according to manufacturer’s instruction, with the exception of the P5 SMART primer that was used instead of S5xx Nextera primer. Each set of 12 samples that was pooled after the PCR reaction was tagmented with a different Nextera N7xx index. Subsequently, the samples were PCR amplified and purified twice using Agencourt AMPure Beads. The libraries were sequenced on a Illumina NextSeq 500, with a custom primer producing read 1 of 20 bp and read 2 (paired end) of 50 bp. Sequencing was performed at the Functional Genomics Unit of the University of Helsinki, Finland.

treatment_protocol: Cells were stimulated for 72h with either a combination of anti-CD3 and anti-CD28 antibodies (positive control, 3 μg and 2 μg/ml; clones 145–2C11 and 37.51; eBioscience), gliadin from wheat (solved in 50mM acetic acid, 20 μg/ml; Sigma cat# G3375), endotoxin-free ovalbumin (negative control, 20 μg/ml; Hyglos), or solvent (negative control, 50mM acetic acid).

value: spleen

value: mixed treatments (non-demultiplexed)


title: T1_C


title: T2_A


title: T1_D


title: T2_C


title: T1_F


title: sample_002


title: sample_006


title: sample_001


title: KO Nuc 2 IP

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description:
KO.Nuc.R2.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: Mouse m6Aseq.xlsx

data_processing:
Library strategy: m6A-seq
The adapters and low quality bases were removed by using cutadapt (v1.1.5).
The fastq files were aligned to the reference genome (mm10 and hg38) using Tophat (v2.1.1).
The m6A peak calling method was modified from published work. The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
PARalyzer was used for PAR-CLIP data peak calling.
Stringtie (v1.3.3b) was used to calculate the FPKM for each gene.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Excel files

source_name: Cortex

extract_protocol:
PAR-CLIP m6A-seq was performed on cells isolated using scraping. m6A-seq and RNAseq were performed on RNA isolated as follows. The nuclear and cytoplasmic fractions of postnatal day 11 (P11) Fmr1KO wild type mouse cortices were isolated using the NE-PER kit (ThermoFisher #78835) following manufacturer’s instructions. The nuclear and cytoplasmic fractions of HEK293T cells were isolated using the following procedure: 3 million HEK293T cells were lysed on ice for 5 minutes using 60μl of NP40 lysis buffer (0.075% Nonidet P40, 10 mM Tris-HCl (pH 7.5), 150mM NaCl, 1:100 cOmplete EDTA-free protease inhibitor (Roche), 1:100 superase inhibitor (ThermoFisher AM2694). The cell lysate was layered over 150μl of chilled sucrose cushion (24% RNase-free sucrose in NP40 lysis buffer) and centrifuged at 4°C for 10 minutes at 15,000g. The supernatant was collected as the cytoplasmic fraction. The pellet was rinsed four times with PBS and collected as the nuclear fraction. The total, cytoplasmic, and nuclear fractions RNA were extracted using Trizol, mRNA was further purified using either one round of the mRNA DIRECT kit (ThermoFisher #61012) and one round of the RiboMinus Eukaryotic kit v2 (ThermoFisher #A15015), or two rounds of the mRNA DIRECT kit. RNA-seq library preparation was performed with TruSeq stranded mRNA sample preparation kit (Illumina).
Illumina TruSeq Stranded mRNA Library Prep Kit.

tag: strain/background

tag: genotype/variation

value: Fmr1 knockout

value: Cortex

tag: age


title: KO Nuc 1 IP

description:
KO.Nuc.R1.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: Mouse m6Aseq.xlsx


title: T1_A


title: T2_D


title: WT Nuc 2 IP

description:
WT.Nuc.R2.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: Mouse m6Aseq.xlsx

value: Wild-type


title: Mecp2 mutated cells [C16]

city: Paris

first: Thierry

last: Bienvenu

address: 24 rue du faubourg St jacques

institute: INSERM

data_processing:
Raw sequencing data in FASTQ format
Read mapping using Tophat 2.0.6 and GRCh37
Alignment using HTSeq Puthon framework and GTF annotation
Gene counts using the R programming langaugae and normalized to RPKM values
Visualization using multi-dimensional scaling plots and heatmaps
Genome_build: DEG identify by DESqe and edgeR
Supplementary_files_format_and_content: count

source_name: Fibroblasts obtained from skin biopsy

growth_protocol: Dulbecco's modified Eagle's medium F-12 HAM supplementaed with 10% fetal bovine serum

extract_protocol:
TruSeq Stranded mRNA kit
Ilumina kit
quantification KAPA library quantification kit and NextSeq 500 sequencing

treatment_protocol: penicillin and streptomycin

value: Mecp2 Mutant clone


title: Mecp2 mutated cells [C11]


title: N134_GFP-miR-431_8

city: New York


title: T2_B


title: WT Nuc 1 IP

description:
WT.Nuc.R1.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: Mouse m6Aseq.xlsx


title: Wild type clone [C15]

value: Wild type clone


title: KO Cyto 2 IP

description:
KO.Cyto.R2.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: Mouse m6Aseq.xlsx


title: Wild type clone [C13]


title: N134_GFP-miR-LacZ_2


title: WT Cyto 2 IP

description:
WT.Cyto.R2.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: Mouse m6Aseq.xlsx


title: N134_GFP-miR-LacZ_1


title: KO Nuc 3

description:
KO.Nuc.R3.input
Fragmented polyA RNA.
processed data file: Mouse RNAseq.xlsx

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.1.5).
The fastq files were aligned to the reference genome (mm10 and hg38) using Tophat (v2.1.1).
The m6A peak calling method was modified from published work. The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
PARalyzer was used for PAR-CLIP data peak calling.
Stringtie (v1.3.3b) was used to calculate the FPKM for each gene.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Excel files


title: Wild type clone  [C10]


title: KO Cyto 1 IP

description:
KO.Cyto.R1.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: Mouse m6Aseq.xlsx


title: WT Cyto 1 IP

description:
WT.Cyto.R1.IP
Fragmented polyA RNA immunoprecipitated with anti-m6A antibody.
processed data file: Mouse m6Aseq.xlsx


title: T47D ATAC-seq noSerum replicate3

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description:
ATAC-seq pair end (PE) replicate 3
processed data file: ATAC-seq_noserum_merged_poissP.bigwig
processed data file: ATAC-seq_noserum_merged_alltags.bigwig
processed data file: ATAC-seq_noserum_merged_peaks.bed
processed data file: ATAC-seq_noserum_merged.bed

data_processing:
The replicates experiments aligned reads were pulled together and processed as unique experiment. Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using Bowtie (Langmead et al., 2009) and aligning parameters of uniqueness (-S –m1 –v2 –t –q). P-values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10-8 and a false discovery rate (FDR) < 1%.
Bam files from different replicates were merged and converted to bed file. Peak calling was done as described above.
Genome_build: h38
Supplementary_files_format_and_content: bigwig, bed

growth_protocol: Human T47D cells (American Type Culture Collection [ATCC]: CRL-2865) were grown in RPMI supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
For nuclei preparation, 5x10e6 cells were washed with cold phosphate-buffered saline (PBS), harvested in cold PBS supplemented with protease inhibitor cocktail (PIC, Roche), and cell pellets obtained by centrifugation at 900xg for 5 min at 4ºC. The cell pellet was gently resuspended in 50 µl of RBS buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with PIC, and then 1.3 ml of RBS buffer - 0.1% Igepal CA-630 was added, followed by centrifugation at 500xg for 10 min at 4ºC. The supernatant was carefully discarded and 1 ml of RBS buffer was added to resuspend the cell nuclei.
For the transposition reaction, 50,000 nuclei were resuspended in 25 µl 2X TD Buffer (Illumina 121-1030), 2.5 µl Tn5 Transposase (Illumina 121-1030) in a final volume of 50 µl. The reaction mix was incubated for 30 min at 37ºC C and DNA purified using the Qiagen Mini-Elute Kit in 10 µl Tris buffer 10mM, pH8.0. Eluate was subjected to PCR amplification in a volume of 50 µl as follow

treatment_protocol: For serum starvation experiments, cells were treated with RPMI supplemented with 10% charcoal-treated FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h.

tag: media

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

tag: antibiotics

value: with antibiotics (100 u/ml penicillin, 100 ug/ml streptomycin)

tag: serum

value: serum-starved


title: KO Nuc 2

description:
KO.Nuc.R2.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: Mouse RNAseq.xlsx
processed data file: Mouse m6Aseq.xlsx


title: T47D ATAC-seq noSerum replicate2

description:
ATAC-seq pair end (PE) replicate 2
processed data file: ATAC-seq_noserum_merged_poissP.bigwig
processed data file: ATAC-seq_noserum_merged_alltags.bigwig
processed data file: ATAC-seq_noserum_merged_peaks.bed
processed data file: ATAC-seq_noserum_merged.bed


title: Mecp2 mutated cells [C3]

tag: genotype


title: WT Nuc 4

description:
WT.Nuc.R4.input
Fragmented polyA RNA.
processed data file: Mouse RNAseq.xlsx


title: T47D ATAC-seq noSerum replicate1

description:
ATAC-seq pair end (PE) replicate 1
processed data file: ATAC-seq_noserum_merged_poissP.bigwig
processed data file: ATAC-seq_noserum_merged_alltags.bigwig
processed data file: ATAC-seq_noserum_merged_peaks.bed
processed data file: ATAC-seq_noserum_merged.bed


title: T47D siADNP TFIIIC chip

description: ChIP-seq single end (SE)

data_processing:
ChIP-seq peak calling. Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using bowtie (Langmead et al., 2009) and aligning parameters of uniqueness (-S âm1 âv2 ât âq). P-values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10-8 and a false discovery rate (FDR) < 1%.
Genome_build: hg38

extract_protocol:
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen).
Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment.

tag: antibody

value: in house anti-GTF3C2 rabbit polyclonal


title: WT Nuc 3

description:
WT.Nuc.R3.input
Fragmented polyA RNA.
processed data file: Mouse RNAseq.xlsx

tag: tissue


title: KO Nuc 4

description:
KO.Nuc.R4.input
Fragmented polyA RNA.
processed data file: Mouse RNAseq.xlsx


title: KO Nuc 1

description:
KO.Nuc.R1.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: Mouse RNAseq.xlsx
processed data file: Mouse m6Aseq.xlsx


title: WT Nuc 2

description:
WT.Nuc.R2.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: Mouse RNAseq.xlsx
processed data file: Mouse m6Aseq.xlsx


title: T47D H3K27ac noSerum

description: ChIP-seq single end (SE)

value: Mouse Monoclonal anti-H3K27ac Millipore Cat. 17-683. Lot.2626032


title: T47D siCTRL TFIIIC chip

description: ChIP-seq single end (SE)


title: WT Nuc 1

description:
WT.Nuc.R1.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: Mouse RNAseq.xlsx
processed data file: Mouse m6Aseq.xlsx


title: T47D H3K9ac noSerum

description: ChIP-seq pair end (PE)

value: Rabbit affinity-purified anti-H3K9ac Active Motif 39137 - lot:16918002


title: T47D H3K27ac Serum

description: ChIP-seq single end (SE)

value: RPMI supplemented with 10% FBS

value: non-serum starved


title: KO Cyto 4

description:
KO.Cyto.R4.input
Fragmented polyA RNA.
processed data file: Mouse RNAseq.xlsx


title: T1_B

description: multiple sub-samples (more information found in separete sample information file)


title: KO Cyto 3

description:
KO.Cyto.R3.input
Fragmented polyA RNA.
processed data file: Mouse RNAseq.xlsx


title: KO Cyto 2

description:
KO.Cyto.R2.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: Mouse RNAseq.xlsx
processed data file: Mouse m6Aseq.xlsx


title: T47D H3K9ac Serum

description: ChIP-seq single end (SE)


title: T47D GTF3C1 noSerum

description: ChIP-seq single end (SE)

value: Novus Biologicals (NB100-606570)


title: Total RNA Hippuristanol replicate 2

city: Glasgow

first: Joseph

middle: Alexander

last: Waldron

address: Switchback road

country: United Kingdom

institute: Beatson Institute for Cancer Research

data_processing:
Reads were mapped to the MCF7 specific transcriptome using Bowtie (version 1.1.1), allowing for multi-mapping
expression levels were estimated at both the transcript and gene level using MMSEQ (version 1.0.10)
MMDIFF was used with the standard differential expression analysis to identify mRNAs which change in total RNA expression between control and hippuristanol treated conditions
MMDIFF was used with the difference of difference (DOD) analysis to identify mRNAs for which the log-fold change in expression between control and hippuristanol treated samples differed within the sub-polysomal and polysomal RNA
Genome_build: An MCF7 specific transcriptome was downloaded from http://datasets.pacb.com.s3.amazonaws.com/2015/IsoSeqHumanMCF7Transcriptome/list.html
Supplementary_files_format_and_content: The DE files contain tab seperated values of the output from the differential expression analysis with MMDIFF. The feature_id contains the PacificBiosciences transcript or gene ID. This is followed by the bayes factor and posterior probability. alpha0 is the overall mean log(e) FPKM in control and hippuristanol treated samples when the expression in control and hippuristanol treated samples does not change, i.e. when the posterior probability is below the threshold set of 0.25, whereas alpha1 is the overal mean log(e) FPKM in control and hippuristanol treated samples for transcripts where the expression does change, i.e. when the posterior probability is above the threshold set of 0.25. eta1_0 is the log-fold change (hippuristanol - control) in expression. The final columns are the mean (mu) and standard deviation (sd) of the log(e) FPKM for each individual sample. TD = totals/DMSO(control) and TH = totals/hippuristanol. Each number represents the biological replicate.
Supplementary_files_format_and_content: The DOD files contain tab seperated values of the output from the difference of difference analysis with MMDIFF. The feature_id contains the PacificBiosciences transcript or gene ID. This is followed by the bayes factor and posterior probability. eta1_1 is the log-fold change (hippuristanol - control) in polysomal RNA expression, whereas eta1_2 is the log-fold change (hippuristanol - control) in sub-polysomal RNA expression . The final columns are the mean (mu) and standard deviation (sd) of the log(e) FPKM for each individual sample. PD = polysomal RNA/DMSO(control) and PH = polysomal RNA/hippuristanol, and SD = sub-polysomal RNA/DMSO(control) and SH = sub-polysomal RNA/hippuristanol. Each number represents the biological replicate.

source_name: Adherent breast cancer cell line

growth_protocol: MCF7 cells grown in DMEM, high glucose, GlutaMAX Supplement, pyruvate (ThermoFisher 31966-021), supplemented with 10% FCS

extract_protocol:
Cells were collected by gentle scraping and then lysed in 500 µl lysis buffer (15mM Tris-HCl pH 7.5, 300mM NaCl, 15mM MgCl2, 2mM DTT and 100 µg/ml cycloheximide, 1% Triton X, 1000U/ml SuperaseIn (AM2694)) for 1 min on ice. Lysate was centrifuged at 12,000g for 1 min at 4°C and the supernatant collected. 400 µl was loaded onto a 10-50% sucrose density gradient (15mM Tris-HCl pH 7.5, 300mM NaCl, 15mM MgCl2, 2mM DTT and 100 µg/ml cycloheximide) and centrifuged in a pre-cooled ultra-centrifuge with the SW40 Ti rotor at 38,000 rpm for 2h at 4°C. For total RNA samples, 50 µl lysate was added to 1ml TRIzol (ThermoFisher 15596026) and RNA was extracted as per manufacturer's instructions followed by isopropanol precipitation. Gradients were fractionated and 11 x 1ml fractions were collected and the RNA precipitated overnight at -20°C following the addition of 3ml guanidine HCl (7.7M) and 4ml 100% ethanol. Precipitated RNA was dissolved in 350 µl TE buffer and ethanol precipitated with 500mM ammonium acetate and 1 µl GlycoBlue. RNA was then dissolved in 30 µl Tris-HCl pH 7.5. Equal volumes of RNA from fractions 1-5 and 6-11 were each pooled to form the sub-polysomal and polysomal RNA respectively.
Illumina TrueSeq Stranded mRNA library preparation

treatment_protocol: Cells were treated for 1h with 150nM hippuristanol or an equal volume of DMSO (0.07%) by replenishment of the growth media. Following 1h incubation, cells were treated for 5 mins with 100  g/ml cycloheximide at 37°C before being washed with ice cold PBS containing 100 µg/ml cycloheximide.

tag: strain

tag: molecule type

value: total RNA

value: 150nM hippuristanol


title: Total RNA Hippuristanol replicate 1


title: WT Cyto 4

description:
WT.Cyto.R4.input
Fragmented polyA RNA.
processed data file: Mouse RNAseq.xlsx


title: WT Cyto 1

description:
WT.Cyto.R1.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: Mouse RNAseq.xlsx
processed data file: Mouse m6Aseq.xlsx


title: Sub-polysomal RNA Hippuristanol replicate 3

value: sub-polysomal


title: Total RNA Control replicate 1

value: control


title: Total RNA Control replicate 2


title: Total RNA Control replicate 3


title: Sub-polysomal RNA Hippuristanol replicate 1


title: Sub-polysomal RNA Hippuristanol replicate 2


title: Run2 Wdr5 KO, T12hRescue-rep1

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

description: Dox treated at T12h

data_processing:
All RNA-seq data were mapped to the mm10 genome for mouse using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed, but not single-end data by SAMtools (v1.5).
For RNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files by using “bamCoverage” from deepTools with parameters “--ignoreDuplicates --normalizeUsingRPKM --skipNonCoveredRegions --binSize 50”.
Aligned reads were assembled using Cufflinks (v2.2.1) and assembled transcriptome catalog were used as input for Cuffdiff2 to determine expression levels (FPKM, Fragments Per Kilobase per Million mapped reads) and differential expression between conditions using default options. CummeRbund v2.1 (http://compbio.mit.edu/cummeRbund/) was then used to process, index, and visualize the output of the Cuffdiff2 analyses. Genes with q<0.01 and fold change (FC) >2 were considered to be differentially expressing genes.
Genome_build: mm10
Supplementary_files_format_and_content: expression Count and FPKM data

source_name: Embryoid bodies

growth_protocol: Rx:GFP mESCs were induced to differentiation with SFEBq method (5%KSR in GMEM media)

extract_protocol:
RNA isolation and DNase treatment were according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.

treatment_protocol: 2% matrigel was added at EB day 1. Dox was added at T12h or T48h in hWDR5 inducible groups.

value: Embryoid bodies

tag: cell type

value: embryonic stem cell, Rx:GFP KI

value: Wdr5 KO


title: Sub-polysomal RNA Control replicate 2


title: Sub-polysomal RNA Control replicate 1


title: Total RNA Hippuristanol replicate 3


title: Run2 Wdr5 KO, T48hRescue-rep1

description: Dox treated at T48h


title: Run2 Wdr5 KO, T48hRescue-rep2

description: Dox treated at T48h


title: Run2 Wdr5 KO, T12hRescue-rep2

description: Dox treated at T12h


title: Polysomal RNA Hippuristanol replicate 3

value: polysomal


title: Sub-polysomal RNA Control replicate 3


title: Polysomal RNA Hippuristanol replicate 2


title: Run2 Wdr5 KO-rep 2

description: No Dox


title: Run2 WT-rep2

description: untreated

value: WT


title: Polysomal RNA Hippuristanol replicate 1


title: Run2 WT-rep1

description: untreated


title: Polysomal RNA Control replicate 3


title: WT Cyto 2

description:
WT.Cyto.R2.input
Fragmented polyA RNA.
RNAseq (m6Aseq input)
processed data file: Mouse RNAseq.xlsx
processed data file: Mouse m6Aseq.xlsx

value: Wild-type

value: Cortex


title: WT Cyto 3

description:
WT.Cyto.R3.input
Fragmented polyA RNA.
processed data file: Mouse RNAseq.xlsx


title: Run1 Wdr5 KO, T48hRescue-rep2

description: Dox treated at T48h


title: Polysomal RNA Control replicate 2


title: Run1 Wdr5 KO, T48hRescue-rep1

description: Dox treated at T48h